He was a trainee at Lyon youth academy between the years of 1995-97 during which time he won the Under-15 championship twice, the Under-17 Cup and the reserve team championship. He also captained the French Under-18 side.
He made his professional debut for the club in a 1-1 draw against Montpellier on February 21 1998 aged 18. He went on to play a total of 96 games for the club which included 12 appearances and 2 goals in the Champions League and 7 appearances in the UEFA Cup.
Malbranque was an unused substitute in the final as Lyon won the 2001 French Coupe de la Ligue.
During his time at the club there was a chance to join Arsenal after impressing in a Champions League tie at Highbury and the following tie, a 3-0 victory over Bayern Munich at Stade de Gerland but he rejected the move as he felt he wasn't ready to play in the Premiership.
He eventually made his move to the Premiership in 2001 joining Fulham for a fee believed to be £4.5million making his debut in a 3-2 defeat at Old Trafford against Man Utd and went on to score 10 goals in his first season.
He became a firm favourite during his 5 years at the club playing a total of 211 games and scoring 44 goals including 6 appearances and 3 goals in Fulham's short-lived UEFA Cup campaign during the 2002-03 season. He was the top scorer during the 2002-03 season with 13 goals that helped save Fulham from relegation and was offered the chance to play for Belgium towards the end of the campaign, having not represented the full France side, however he turned it down with the hope that he would eventually break into the full French squad.
On May 13, 2006, after extensive contract talks with the club failed, Malbranque was placed on the transfer list at Fulham after he declared his intentions to leave at the end of his contract. There was rumoured interest from Reading, Middlesbrough, West Ham United, Manchester City, Everton and Newcastle United but he opted to sign for Tottenham Hotspur on the deadline day of the transfer window (August 31 2006) for a fee believed to be £2million despite an injury that would keep him out for approximately 10 weeks.
Malbranque made his debut for Tottenham almost ten weeks after signing for the club on November 8 2006 at White Hart Lane playing 63 minutes in a League Cup 3-1 victory over Port Vale. He scored his first goal for Spurs in an emphatic 5-1 victory over Charlton Athletic at White Hart Lane on December 9 2006.
Malbranque was called into the senior France squad in February 2004 but did not make an appearance during any matches.